Showing : rna-seq • reset
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
8 days ago • updated 7 days ago Dylan.Sheerin • 0
2
votes
3
replies
251
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 days ago by ★ 4.1k • written 13 days ago by • 0
3
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3
replies
365
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permutation test in edgeR
rna-seq edgeR
updated 25 days ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
916
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 5 months ago by ★ 4.1k • written 6.1 years ago by • 0
0
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2
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319
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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4
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730
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago ar14g12 • 0
0
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2
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3.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
2
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3
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1.7k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
0
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3
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684
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
3
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4
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890
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
0
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3
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707
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
5
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7
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1.2k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
0
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3
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727
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Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 12 months ago by 65k • written 12 months ago by • 0
0
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3
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874
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 65k • written 12 months ago by • 0
1
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1
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1.4k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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1
reply
704
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 13 months ago by 65k • written 13 months ago by • 0
2
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2
replies
738
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
682
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
734
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 17 months ago by 42k • written 18 months ago by • 0
5
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9
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1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago • updated 21 months ago Yang Shi ▴ 10
2
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2
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1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
22 months ago Yang Shi ▴ 10
0
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0
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883
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
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2
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1.0k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 22 months ago by 50k • written 22 months ago by • 0
0
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2
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2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
3
votes
3
replies
3.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.2 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
5
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5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.2 years ago • updated 2.0 years ago 9906201a ▴ 20
1
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5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago • updated 2.2 years ago Lucy ▴ 60
1
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3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
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5
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3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
0
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1
reply
908
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.3 years ago by 50k • written 2.3 years ago by • 0
1
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1
reply
2.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.7 years ago by ▴ 10 • written 3.9 years ago by ▴ 10
0
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5
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1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
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0
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922
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago slcno • 0
3
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5
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2.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.9 years ago by 42k • written 2.9 years ago by ▴ 60
0
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1
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1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
2
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3
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1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.0 years ago by 50k • written 3.0 years ago by • 0
5
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2
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22k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.3 years ago by ▴ 30
1
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1
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1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.0 years ago by ★ 1.0k • written 3.0 years ago by ▴ 20
3
votes
4
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1.1k
views
need help regarding differential expression analysis
rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by ▴ 20
0
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0
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960
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
1
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4
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3.8k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.1 years ago by ★ 1.0k • written 6.6 years ago by • 0
3
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4
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1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.1 years ago Antonio M. • 0
1
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2
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1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
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7
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1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.2 years ago decppced • 0
1
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3
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857
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
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0
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882
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
3
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9
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2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.4 years ago Pufall, Miles A ▴ 30
0
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1
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1.1k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
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2
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1.6k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 70
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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